fs dt recon intro

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					Introduction to
Diffusion MRI
processing
Lilla Zöllei
dt_recon
Required Arguments:
 --i invol
 --s subjectid
 --o outputdir


   Example: dt_recon --i
    dt_recon --i 6-1025.dcm --s M111 --o dti

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Main processing steps
   # Eddy current and motion correction
       (FSL   eddy_correct)
   # Tensor fitting
       tensor.nii,eigvals.nii. eigvec?.nii
       set of scalar maps: adc, fa, ra, vr, ivc

   # Registration to anatomical space
       (FSL   flirt to lowb)
   # Mapping mask, FA to Talairach space
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Other Arguments (Optional)
--b bvals bvecs
--info-dump infodump.dat
         use info dump created by unpacksdcmdir or dcmunpack
--ecref TP
         use TP as 0-based reference time points for EC
--no-ec
         turn off eddy/motion correction
--no-reg
         do not register to subject or resample to talairach
--no-tal
         do not resample FA to talairch space
--sd subjectsdir
         specify subjects dir (default env SUBJECTS_DIR)
--eres-save
         save resdidual error (dwires and eres)
--pca
         run PCA/SVD analysis on eres (saves in pca-eres dir)
--prune_thr thr
         set threshold for masking (default is FLT_MIN)
--debug
         print out lots of info
--version
         print version of this script and exit
--help
         voluminous bits of wisdom
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The diffusion process




              http://pubs.niaaa.nih.gov/publications/arh27-2/146-152.htm
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Examples of scalar maps
   FA: fractional anisotropy (fiber
                                               
                                              3        
                                                    1
                                                          2
                                                                 2     3    
                                                                        2           2
                                                                                      
                                              2
                                                             1  2  3
                                                               2    2     2           
                                                                                      
    density, axonal diameter, myelination                                            
    in WM)
                                                        var  
   RA: relative anisotropy
   VR: volume ratio                                12 3         3
   IVC: inter-voxel correlation (diffusion
    orientation agreement in neighbors)
   ADC: apparent diffusion coefficient
    (magnitude of diffusion; low value       ln S 0 S1  b1  b0 
    organized tracts)
   RD: radial diffusivity                          2  3          2
   AD: axial diffusivity                                 1
   …



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FA




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ADC




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IVC




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Tractography examples
   Trackvis and Diffusion Toolkit
    (http://www.trackvis.org/)




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CST on (color) FA map




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END




Feb 1, 2010   13
Stages:
   1. Convert dicom to nifti (creates dwi.nii)
   2. Eddy current and motion correction using FSLs eddy_correct,
     creates dwi-ec.nii. Can take 1-2 hours.
   3. DTI GLM Fit and tensor construction. Includes creation of:
     tensor.nii -- maps of the tensor (9 frames)
     eigvals.nii -- maps of the eigenvalues
     eigvec?.nii -- maps of the eigenvectors
     adc.nii -- apparent diffusion coefficient
     fa.nii -- fractional anisotropy
     ra.nii -- relative anisotropy
     vr.nii -- volume ratio
     ivc.nii -- intervoxel correlation
     lowb.nii -- Low B
     bvals.dat -- bvalues
     bvecs.dat -- directions
     Also creates glm-related images:
       beta.nii - regression coefficients
       eres.nii - residual error (log of dwi intensity)
       rvar.nii - residual variance (log)
       rstd.nii - residual stddev (log)
       dwires.nii - residual error (dwi intensity)
       dwirvar.nii - residual variance (dwi intensity)
   4. Registration of lowb to same-subject anatomical using
     FSLs flirt (creates mask.nii and register.dat)
   5. Map FA to talairach space (creates fa-tal.nii)
   Example usage:
   dt_recon --i 6-1025.dcm --s M87102113 --o dti
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After dt_recon
   # Check registration
   tkregister2 --mov dti/lowb.nii --reg dti/register.dat \
     --surf orig --tag

   # View FA on the subject's anat:
   tkmedit M87102113 orig.mgz -overlay dti/fa.nii \
     -overlay-reg dti/register.dat

   # View FA on fsaverage
   tkmedit fsaverage orig.mgz -overlay dti/fa-tal.nii

   # Group/Higher level GLM analysis:
   # Concatenate fa from individuals into one file
   # Make sure the order agrees with the fsgd below
   mri_concat */fa-tal.nii --o group-fa-tal.nii
   # Create a mask:
   mri_concat */mask-tal.nii --o group-masksum-tal.nii --mean
   mri_binarize --i group-masksum-tal.nii --min .999 --o group-mask-tal.nii
   # GLM Fit
   mri_glmfit --y group-fa-tal.nii --mask group-mask-tal.nii\
     --fsgd your.fsgd --C contrast --glm groupanadir


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